Downstream waves recover positive correlations of estimated elongation times with 1 / tAI.

In experiments using CHX pretreatment, the combined enrichment of each codon identity at the A-, P-, and E-sites before the introduction of CHX can be estimated by adding the net area of the codon’s downstream wave back to the total remaining enrichments at the three tRNA binding sites. This sum correlates positively with 1 / tAI in all CHX experiments (purple dots), recovering the positive correlations counterintutively absent at the tRNA binding sites alone in these experiments (green dots). Positive correlations are statistically significant (p < 0.05, one-tailed) in most experiments. This suggests that non-optimal codons were being translated less quickly than optimal codons in CHX experiments before the introduction of CHX disrupted these dynamics.